Contacts of the helix formed by residues 13 - 22 (chain T) in PDB entry 5GAG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 13 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1266A G 3.1 38.3 + - - -
2012A G 5.7 1.2 + - - -
12T SER* 1.3 79.0 + - - +
14T ALA* 1.3 64.4 + - - +
15T GLN* 2.9 5.5 + - - -
16T LYS* 2.6 40.6 + - - +
17T VAL* 3.5 18.5 + - - +
99T ARG* 4.2 14.8 - - - +
101T SER* 4.0 1.2 - - - -
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Residues in contact with ALA 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T SER 3.8 1.2 + - - -
13T SER* 1.3 72.5 - - - +
15T GLN* 1.3 58.2 + - - +
17T VAL 3.2 1.6 + - - -
18T ARG* 3.0 49.9 + - - +
76T VAL* 3.7 17.6 - - + +
77T ASP 3.8 13.9 - - - +
78T GLU* 3.5 34.6 - - + +
99T ARG* 5.3 1.8 - - - +
100T THR 4.3 2.8 + - - -
101T SER* 3.9 4.8 - - - -
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Residues in contact with GLN 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266A G 3.1 57.9 + - - +
3235A MG 3.9 6.8 - - - -
13T SER* 2.9 7.7 + - - +
14T ALA* 1.3 81.3 - - - +
16T LYS* 1.3 60.5 + - - +
17T VAL 3.6 0.2 + - - -
18T ARG* 3.8 17.9 + - - +
19T LEU* 3.8 22.5 + - + +
78T GLU* 6.2 0.2 - - - +
17b ARG* 3.2 43.8 + - - +
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Residues in contact with LYS 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266A G 3.7 29.2 + - + +
2011A U 3.2 29.5 + - - +
2012A G 2.8 61.0 + - - -
12T SER* 4.4 9.0 - - - +
13T SER* 2.6 32.0 + - - +
15T GLN* 1.3 71.7 - - - +
17T VAL* 1.3 64.8 + - - +
19T LEU* 3.6 22.6 - - - +
20T VAL* 4.1 4.0 + - - +
41T LYS* 5.2 3.8 + - - +
43T ALA* 4.1 9.1 - - + +
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Residues in contact with VAL 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T SER* 3.5 28.9 - - - +
13T SER 3.5 10.1 + - - +
14T ALA 3.2 7.4 + - - +
16T LYS* 1.3 74.7 - - - +
18T ARG* 1.3 67.5 + - - +
19T LEU 3.2 0.2 - - - -
20T VAL* 3.1 6.2 + - - +
21T ALA* 2.9 18.6 + - + +
43T ALA* 3.7 16.6 - - + -
46T LEU* 4.6 6.1 - - + -
47T VAL* 3.9 23.1 - - + -
76T VAL* 3.5 27.8 - - + -
101T SER* 4.1 7.2 - - - +
103T ILE* 4.3 9.0 - - + -
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Residues in contact with ARG 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A C 2.4 31.9 + - - -
518A G 2.8 50.9 + - - +
14T ALA* 3.0 35.9 + - - +
15T GLN* 4.0 16.6 - - - +
17T VAL* 1.3 76.0 - - - +
19T LEU* 1.3 63.9 + - + +
21T ALA* 3.0 8.0 + - + -
22T ASP* 2.9 40.9 + - - +
76T VAL* 3.3 36.8 + - + +
77T ASP* 4.8 2.8 - - - +
78T GLU* 4.9 2.6 + - - -
17b ARG* 5.9 1.4 - - - +
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Residues in contact with LEU 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T GLN* 3.8 14.7 + - + +
16T LYS* 3.6 15.4 + - - +
17T VAL 3.2 0.2 - - - -
18T ARG* 1.3 79.2 - - + +
20T VAL* 1.3 61.7 + - - +
22T ASP* 3.9 14.0 + - - +
23T LEU* 4.1 5.9 - - - +
41T LYS* 4.3 19.5 - - - +
17b ARG 5.7 1.1 - - - +
20b ASP* 3.2 39.5 - - + +
21b ALA* 4.2 7.8 - - - +
22b LEU* 3.7 26.3 + - + +
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Residues in contact with VAL 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T LYS 4.6 1.3 - - - +
17T VAL 3.1 7.5 + - - +
19T LEU* 1.3 74.4 - - - +
21T ALA* 1.3 59.4 + - - +
22T ASP 2.8 11.1 + - - -
23T LEU* 2.9 24.8 + - + +
24T ILE* 4.0 4.0 + - - +
36T LEU* 3.6 30.7 - - + -
39T THR* 4.3 4.9 - - + -
41T LYS* 3.6 39.9 - - + -
43T ALA* 4.0 14.6 - - + -
44T ALA* 4.0 9.4 - - + +
47T VAL* 4.1 11.7 - - + -
22b LEU* 3.9 12.6 - - + -
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Residues in contact with ALA 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T VAL 2.9 16.3 + - - +
18T ARG* 3.0 8.5 + - - +
20T VAL* 1.3 77.9 - - - +
22T ASP* 1.3 63.6 + - - +
23T LEU 3.4 0.2 - - - -
24T ILE* 3.6 20.4 - - - +
25T ARG* 3.7 6.5 + - - +
47T VAL* 4.6 9.4 - - + -
74T ILE* 3.8 37.3 - - + +
75T PHE* 5.9 0.4 - - - -
76T VAL* 4.5 13.5 - - + -
103T ILE* 5.8 0.2 - - + -
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Residues in contact with ASP 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A U 5.4 3.7 + - - -
18T ARG* 2.9 35.4 - - - +
19T LEU* 3.9 10.9 + - - +
20T VAL 2.8 0.6 + - - -
21T ALA* 1.3 79.6 - - - +
23T LEU* 1.3 65.7 + - + +
24T ILE 3.2 2.3 + - - -
25T ARG* 3.1 43.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il